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  <div class="section" id="module-pysimm.amber">
<span id="pysimm-amber-module"></span><h1>pysimm.amber module<a class="headerlink" href="#module-pysimm.amber" title="Permalink to this headline">¶</a></h1>
<dl class="function">
<dt id="pysimm.amber.calc_charges">
<code class="descclassname">pysimm.amber.</code><code class="descname">calc_charges</code><span class="sig-paren">(</span><em>s</em>, <em>charge_method='bcc'</em>, <em>cleanup=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/amber.html#calc_charges"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.amber.calc_charges" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates charges using antechamber. Defaults to am1-bcc charges.</p>
<table class="docutils field-list" frame="void" rules="none">
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<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>s</strong> &#8211; System for which to calculate charges. System object is updated in place</li>
<li><strong>charge_method</strong> &#8211; name of charge derivation method to use (default: bcc)</li>
<li><strong>cleanup</strong> &#8211; removes temporary files created by antechamber (default: True)</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">None</p>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="function">
<dt id="pysimm.amber.cleanup_antechamber">
<code class="descclassname">pysimm.amber.</code><code class="descname">cleanup_antechamber</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/amber.html#cleanup_antechamber"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.amber.cleanup_antechamber" title="Permalink to this definition">¶</a></dt>
<dd><p>Removes temporary files created by antechamber and pysimm.</p>
<table class="docutils field-list" frame="void" rules="none">
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<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>None</strong> &#8211; </td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">None</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="function">
<dt id="pysimm.amber.get_forcefield_types">
<code class="descclassname">pysimm.amber.</code><code class="descname">get_forcefield_types</code><span class="sig-paren">(</span><em>s</em>, <em>types='gaff'</em>, <em>f=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pysimm/amber.html#get_forcefield_types"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pysimm.amber.get_forcefield_types" title="Permalink to this definition">¶</a></dt>
<dd><p>Uses antechamber to determine atom types. Defaults to GAFF atom types. Retrieves <a class="reference internal" href="pysimm.system.html#pysimm.system.ParticleType" title="pysimm.system.ParticleType"><code class="xref py py-class docutils literal"><span class="pre">ParticleType</span></code></a> objects from force field is provided</p>
<table class="docutils field-list" frame="void" rules="none">
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<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>s</strong> &#8211; <a class="reference internal" href="pysimm.system.html#pysimm.system.System" title="pysimm.system.System"><code class="xref py py-class docutils literal"><span class="pre">System</span></code></a> for which to type</li>
<li><strong>types</strong> &#8211; name of atom types to use (default: gaff)</li>
<li><strong>f</strong> &#8211; forcefield object to retrieve <a class="reference internal" href="pysimm.system.html#pysimm.system.ParticleType" title="pysimm.system.ParticleType"><code class="xref py py-class docutils literal"><span class="pre">ParticleType</span></code></a> objects from if not present in s (default: None)</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">None</p>
</td>
</tr>
</tbody>
</table>
</dd></dl>

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